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Top Level Haplogroup Markers

All markers shown, except those in parentheses, are present at ≥80% in the top level haplogroups of the current Mitomap dataset. Parentheses indicate variants which are ≥50% but <80%. Lowercase letters indicate transversions (e.g., 3516a). Ancestral variants which also serve as top level haplogroup branch markers in Phylotree are shown in italics. Markers matching the rCRS reference value are indicated with "=" (e.g., 263A=); while these latter markers are important to delineate the haplogroup in the phylogenetic tree, they will not usually be listed in genetic test reports because they are identical to the reference rCRS sequence.

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Lineage Top Level Haplogroup # Seqs Ancestral Marker Motif
(the " RSRS50")
HG Markers Other Selected Markers
L L0 1499 247A, 750G, 769A, 825a, 1018A, 2758A, 2885C, 3594T, 4104G, 4312T, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10664T, 10688A, 10810C, 10873C, 10915C, 11719A, 11914A, 12705T, 13105G, 13276G, 13506T, 13650T, 14766T, 15326G, 16187T, 16189C, 16223T, 16230G, 16311C

(73G, 146C, 152C, 195C, 1438G, 2706G, 16519C)

1048T, 3516a, 5442C, 6185C, 9042T, 9347G, 9755A, 10589A, 12007A, 12720G

(189G, 514_515delCA, 4586C, 5460A, 9818T, 16172C)
(263A=)
L L1 873 73G, 152C, 195C, 247A, 263G, 750G, 769A, 825a, 1018A, 2706G, 2758A, 2885C, 3594T, 4104G, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10688A, 10810C, 10873C, 11719A, 12705T, 13105G, 13506T, 13650T, 14766T, 15326G, 16187T, 16189C, 16223T, 16278T, 16311C, 16519C

(1438G, 16129A)

182T, 3666A, 7055G, 7389C, 13789C, 14178C, 14560A

(151T, 186A, 189C, 316A, 514_515delCA, 2394del, 5951G, 6071C, 8027A, 9072G, 10321C, 10586A, 12810G, 13485G, 14000a, 14911T, 16294T, 16360T)
L L5 39 73G, 152C, 247A, 263G, 750G, 769A, 825a, 1018A, 1438G, 2706G, 3594T, 4104G, 4769G, 7028T, 7256T, 7521A, 8655T, 8701G, 8860G, 9540C, 10398G, 10688A, 10810C, 10873C, 11719A, 12705T, 13506T, 13650T, 14766T, 15326G, 16129A, 16223T, 16278T, 16311C

(195C, 13105G, 16189C)
182T, 709A, 851G, 1822C, 3423C, 5111T, 5147A, 6182A, 6297C, 7972G, 8155A, 8188G, 8582T, 9305A, 11025C, 11881T, 12236A, 12432T, 12950G, 13722G, 14212C, 14239T, 14581C, 14905A, 14971C, 15217A, 15884A, 16148T, 16166G

(514_515delCA, 5656G, 7424G, 9329A, 16183c, 16355T, 16362C)

Length variants in the 455-459 region [459CC or 455TTC or 455TTTC]
L L2 1317 73G, 146C, 152C, 195C, 263G, 750G, 769A, 1018A, 1438G, 2706G, 3594T, 4104G, 4769G, 7028T, 7256T, 7521A, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 13650T, 14766T, 15326G, 16223T, 16278T

(11914A)

146C, 152C, 2416C, 8206A, 9221G, 10115C, 11944C, 13590A, 15301A, 16390A

(2789T, 7175C, 7274T, 7771G, 12693G, 13803G, 14566G, 15784C, 16294T, 16309G)
150C=, 16311T=
L L6 12 73G, 146C, 152C, 263G, 750G, 769A, 1018A, 1438G, 2706G, 3594T, 4769G, 7028T, 7256T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 13650T, 14766T, 15326G, 16223T, 16278T, 16311C, 16519C 146C, 152C, 182T, 185c, 709A, 770T, 961C, 1461G, 4964T, 5267C, 6002G, 6284G, 9332T, 10978G, 11116C, 11743T, 12771A, 13710G, 14791T, 14959G, 15244G, 15289C, 15301A, 15499T, 16048A, 16224C

(265C, [309_310insCT +310C, 310C +310_311insTC, or 315insC])

L L4 104 73G, 263G, 750G, 769A, 1018A, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T, 16311C

(146C, 16519C)

3918A, 15301A, 16362C

(244G, 315insC, 1413C, 8104C, 9855G, 12609C, 13470G, 16293t, 16355T, 16399G)
3594C=
Additional markers for branches: L4a: 195C, 5460A; L4b2: 146C
L L3 2129 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)

15301A

(150T, 514_515delCA)
769G=, 1018G=, 3594C=, 16311T=
M M 5014 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)
489C, 10400T, 14783C, 15043A, 15301A Additional markers for branches:

M7: 4071T, 6455T, 9824C (199C).

M8: 4715G, 6179A, 7196A, 8584A, 8684T, 14470C, 15487T, 16298C, 16319A (310C, 2835T, 16184T). Haplogroups C & Z are in the M8 branch.

M9: 1041G, 3394C, 4491A, 14308C, 16234T, 16362C (16316G). Haplogroup E is in the M9 branch.
M Q 174 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16129A, 16311C

(146C, 16223T)
489C, 4117C, 5460A, 5843G, 8790A, 10400T, 12940A, 13500C, 14783C, 15043A, 15301A, 16241G

(89C, 92A, 8964T, 14025C, 16144C, 16148T, 16265c, 16343G)
M C 1609 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 11914A, 12705T, 14766T, 15326G, 16223T

(16519C)

248del or 249del, 489C, 3552a, 4715G, 7196a, 8584A, 9545G, 10400T, 13263G, 14318C, 14783C, 15043A, 15301A, 15487t, 16223T, 16298C, 16327T

(310C)
M Z 178 73G, 152C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)

248del or 249del, 489C, 4715G, 6752G, 7196a, 8584A, 9090C, 10400T, 14783C, 15043A, 15301A, 15487t, 15784C, 16185T, 16223T, 16260T, 16298C

(151T)

M E 450 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 15326G, 16223T, 16519C 489C, 3027C, 3705A, 4248C, 4491A, 7598A, 10400T, 10834T, 13254C, 13626T, 14577C, 14783C, 15043A, 15301A, 16362C, 16390A

(6620C, 16291T)

M G 428 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

489C, 709A, 4833G, 5108C, 10400T, 14569A, 14783C, 15043A, 15301A, 16362C

(5601T, 9575A, 13563G)

M D 2282 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T

489C, 3010A, 4883T, 5178a, 8414T, 10400T, 14668T, 14783C, 15043A, 15301A, 16223T, 16362C, 16223T

N N 744 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T

(16519C)
- 8701A=, 9540T=, 10398A=, 10400C=, 10873T=, 15301G=

Additional markers for branches:

N1: 1719A, 10238C, 12501A (152C). Haplogroup I is in the N1 branch.

N2: 150T (195C, 335d, 6752G, 8701G, 10583G, 13437C, 14560A, 16193T). Haplogroup W is in the N2 branch.

N9: 150T, 5231A, 5417A, 12358G, 12372A, 16257A (310C, 16261T). Haplogroup Y is in the N9 branch.
N O 8 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T

(152C, 16189C, 16519C)

6755A, 9140T, 16213A

(794C, 5563A, 16183c)

N S 47 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G

(152C, 16223T)

8404C
N I 699 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 12705T, 14766T, 15326G, 16129A, 16223T, 16519C

199C, 204C, 250C, 1719A, 4529t, 8251A, 10034C, 10238C, 12501A, 13780G, 15043A, 15924G, 16129A, 16223T, 16391A
N W 521 73G, 195C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T, 16519C 189G, 195C, 204C, 207A, 709A, 1243C, 3505G, 5046A, 5460A, 8251A, 8994A, 11674T, 11947G, 12414C, 15884c, 16292T

(194T)

N Y 133 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 12705T, 14766T, 15326G

(146C, 16519C)
5417A, 8392A, 10398G, 14178C, 14693G, 16126C, 16231C

(310C, 3834A, 7933G)
16223C=

Additional markers for branch Y1:146C, 3834A, 7933G
N A 1340 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T

(146C)

235G, 514_515delCA, 663G, 1736G, 4248C, 4824G, 8794T, 16223T, 16290T, 16319A, 16362C

(153G, 310C, 8027A, 12007A, 16111T)

N X 459 73G, 195C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16189C, 16223T, 16278T, 16519C 1719A, 6221C, 6371T, 13966G, 14470C, 16189C, 16223T, 16278T

(153G, 225A, 16183c)

Additional markers for branch X1: 146C, 14587G; absent in X1: 195C, 225A, 1719A
N R 1012 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 14766T, 15326G

(73G, 11719A, 16519C)
- 12705C=, 16223C=

Additional markers for branches:

R0:64T, 2442C, 3847C, 13188T, 16362C (310C, 16126C). Haplogroups HV, H, & V are in the R0 branch.

R9: 73G, 3970T, 11719A, 13928C, 16304C (1541C, 12714C, 16309G, 16390A). Haplogroup F is in the R9 branch.
N P 142 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G

(152C, 16519C)

15607G  
N HV 723 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 15326G (310C)

14766C=
N H 8971 263G, 750G, 1438G, 4769G, 8860G, 15326G

(16519C)

- 2706A=, 7028C=
N V 677 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 15326G 72C, 4580A, 15904T, 16298C

(310C)

N J 2275 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 14766T, 15326G 295T, 489C, 4216C, 11251G, 12612G, 13708A, 15452a, 16069T, 16126C

(462T, 3010A, 14798C)

N T 2163 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, 16519C 709A, 1888A, 4216C, 4917G, 8697A, 10463C, 11251G, 13368A, 14905A, 15452a, 15607G, 15928A, 16126C, 16294T

(11812G, 14233G)

10398A=
N F 1553 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G

(16129A, 16519C)

248del or 249del, 3970T, 6392C, 10310A, 13928C, 16304C

(514_515delCA, 6962A, 9053A, 10609C, 12406A, 12882T, 13759A)

N B 3982 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, 16189C, 16519C

(146C)
16183C, 16189C, 16217C Additional markers for branches:

B2: 8271 9bp deletion [8271_8279del or 8281_8289del], 146T=, 499A, 827G, 3547G, 4820A, 4977C, 6473T, 9950C, 10398A=, 11177T, 13590A, 15535T (310C)

B4: (8271 9bp deletion [8271_8279del or 8281_8289del], 514_515delCA, 5465C, 6719C, 9123A, 10238C, 10398A=, 12239T, 14022G, 15746G, 16182C, 16247G, 16261T)

B5: 146T=, 709A, 8584A, 9950C, 10398G, 16140C, 16217T=, (210G, 514_515delCA, 3537G, 6960T, 15235G, 16266A)
N U 4080 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G

11467G, 12308G, 12372A
N K 1775 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 14766T, 15326G, 16311C, 16519C 1189C, 1811G, 3480G, 9055A, 9698C, 10550G, 11299C, 11467G, 12308G, 12372A, 14167T, 14798C, 16224C, 16311C

(315insC, 497T)

* Ancestral SNPs are common throughout the human mtDNA tree. These ancestral variants, the "RSRS50", are: 73G, 146C, 152C, 195C, 247A, 263G, 750G, 769A, 825A, 1018A, 1438G, 2706G, 2758A, 2885C, 3594T, 4104G, 4312T, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10664T, 10688A, 10810C, 10873C, 10915C, 11719A, 11914A, 12705T, 13105G, 13276G, 13506T, 13650T, 14766T, 15326G, 16129A, 16187T, 16189C, 16223T, 16230G, 16278T, 16311C, 16519C. Additionally, the RSRS ancestor sequence has two single base deletions, 523d & 524d, which are located at the end of a string of CA repeats. Indels in this region are variously notated and common. These two deleted bases are not indexed in Mitomap's "RSRS50" set and are among those variants specifically excluded by Phylotree in the construction of their master tree.

Topic revision: r23 - 20 Feb 2019, MarieLott

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